An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk.

ABSTRACT: Modular response analysis (MRA) is a widely used inference technique developed to uncover directions and strengths of connections in molecular networks under a steady-state condition by means of perturbation experiments. We devised several extensions of this methodology to search genomic data for new associations with a biological network inferred by MRA, to improve the predictive accuracy of MRA-inferred networks, and to estimate confidence intervals of MRA parameters from datasets with low numbers of replicates. The classical MRA computations and their extensions were implemented in a freely available R package called aiMeRA ( https://github.com/bioinfo-ircm/aiMeRA/ ). We illustrated the application of our package by assessing the crosstalk between estrogen and retinoic acid receptors, t

SUBMITTER: Jimenez-Dominguez G 

PROVIDER: S-EPMC8012374 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature